Contacts of the strand formed by residues 465 - 469 (chain A) in PDB entry 3CMM
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 465 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A SER 2.9 9.2 + - - +
436A LYS* 3.8 33.1 - - + +
437A VAL* 3.1 24.5 + - - +
459A GLY* 3.3 11.9 + - - -
463A ASP 4.9 1.8 - - - -
464A GLY* 1.3 79.6 - - - +
466A ILE* 1.3 69.4 + - - +
467A VAL* 4.0 26.2 - - + -
512A LYS* 3.5 16.8 - - + +
514A ASN* 6.2 1.6 - - + -
532A PHE* 5.1 0.7 + - - -
535A SER* 3.6 26.5 - - - -
536A LEU* 4.1 13.2 - - + +
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Residues in contact with ILE 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A VAL* 3.6 18.6 - - + -
439A LEU* 5.0 0.4 - - + -
450A LEU* 4.0 13.7 - - + -
453A TRP* 4.0 30.1 - - + -
458A LEU* 3.4 28.3 - - + +
459A GLY* 4.5 0.4 - - - -
465A TYR* 1.3 79.0 - - - +
467A VAL* 1.3 70.5 + - - +
468A VAL* 3.9 13.9 - - + -
509A LEU* 4.3 17.7 - - + -
512A LYS 3.1 5.7 + - - +
513A ILE* 3.5 26.8 - - + -
514A ASN* 2.8 28.6 + - - +
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Residues in contact with VAL 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A VAL 2.9 11.0 + - - +
438A PHE* 3.3 26.5 - - + -
439A LEU* 2.7 33.6 + - - +
465A TYR* 4.0 22.7 - - + -
466A ILE* 1.3 78.1 - - - +
468A VAL* 1.3 59.5 + - - +
469A THR* 4.3 0.9 - - + -
514A ASN* 3.4 23.3 - - + +
516A LYS* 4.1 26.2 - - + -
532A PHE* 4.1 20.9 - - + -
536A LEU* 5.1 0.9 - - + -
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Residues in contact with VAL 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A LEU* 3.1 33.0 - - + +
441A GLY 3.8 9.9 - - - +
442A SER* 4.2 12.6 - - - +
450A LEU* 3.9 23.1 - - + -
466A ILE* 3.9 7.9 - - + -
467A VAL* 1.3 76.8 - - - +
469A THR* 1.3 64.8 + - - +
495A SER* 4.1 11.3 - - - +
499A ALA* 5.3 0.4 - - + -
513A ILE* 3.8 25.8 - - + -
514A ASN 3.2 4.9 + - - +
515A ALA* 3.7 5.5 - - + -
516A LYS 2.8 27.1 + - - +
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Residues in contact with THR 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438A PHE* 3.6 15.2 - - + -
439A LEU 3.0 5.9 + - - -
440A VAL* 4.2 5.4 - - - +
441A GLY* 2.7 32.6 + - - -
467A VAL* 4.3 0.2 - - + -
468A VAL* 1.3 74.8 - - - +
470A ASP* 1.3 62.9 + - - +
495A SER* 4.5 1.8 - - - -
516A LYS* 3.2 34.5 - - + -
518A ASP 3.5 13.7 + - - +
520A VAL* 3.6 21.7 - - - +
528A PHE* 3.4 25.8 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il